Regulators have opened dozens of investigations into UK Muslim charities over the last five years following weapons discoveries, the unmasking of extremists in religious schools and allegations of terrorist financing, analysis of official data shows.

The Charity Commission publicly announced some 125 new inquiries of charities in England and Wales since the start of 2014, with more than 35 related to Muslim groups and causes. Documents show some of the investigations are related to allegations of extremist preaching at charity-run schools and suspicions that money raised for Syrian relief efforts was being funnelled to terrorists.

The new investigations were among those launched after two damning reports in 2013 and 2014 that criticised failures by the commission to regulate the sector and crack down on abuse of the system. A report by UK lawmakers in 2014 found that the commission was “too willing to accept what charities tell it, without verifying or challenging the claims made”. The government’s auditor said last year that it had “improved significantly” since 2013.

The regulator – which says the abuse of charities for terrorist purposes was one of its three priority areas - announced in March that it had launched an investigation following the jailing of a school administrator who tried to recruit a 300-strong children’s army from a school and mosque, both regulated by the Charity Commission.

Umar Haque, 25, showed beheading videos during Islamic studies classes he headed at the mosque and a fee-paying private Islamic school. After Haque was jailed, police revealed that 35 youngsters were undergoing long-term supervision by authorities – but the regulator said nobody had raised any concerns about his work at any charity.

“The public expect charities, particularly those working with children and young people, to be safe places from abuse or harm,” the regulator said in a statement announcing the inquiry launch. “This was not the case here.”

The regulator in July launched an inquiry into a school in southeast London – once dubbed the Muslim Eton – after £400,000 and bladed weapons were found at a flat in the grounds of the boarding school. The headteacher of the Darul Uloom school was arrested on suspicion of money laundering and the school reached an agreement with the education authorities to prevent its immediate closure.

Another Muslim education group, the Fazal Ellahi Charitable Trust that ran a mosque and religious classes, was targeted for a new investigation this year and its account frozen because of concerns about terrorism.

It was removed from the charity’s register in 2009 after it stopped filing accounts but it later emerged it was still running a mosque after an imam was convicted of six counts of encouraging terrorism and two of encouraging support for a proscribed organisation during a series of classes to children. The inquiry is ongoing.

The publicly announced number of inquiries represent a fraction of those launched, according to documents released by the regulator.